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While visiting with her family in San Diego, Scully became involved with a suicide investigation that became a murder investigation centered on Marshall Sim, who apparently murdered his wife. Scully was disturbed by an uncanny resemblance between Emily and her deceased sister Melissa. She was further disturbed by unusual phone calls exhorting help for the little girl that sounded just like Melissa's voice. Scully began investigating further with aid from John Kresge and came to the conclusion that Emily was Melissa's daughter. Scully's brother Bill and mother were aghast that Melissa had given birth to a daughter without telling anyone. However, another test was run that proved Melissa not to be the mother. Rather, Scully herself was the mother. (TXF: "Christmas Carol")

With help from Mulder, Scully began investigating more into the mystery of Emily. They concluded that Emily must have been conceived with Scully's ova that was harvested during her abduction nearly four years earlier. Conclusive proof of her involvement with the conspiracy was found when a strange green mark was found on the back of her neck that, when cut open, released the noxious, green blood found in aliens. Further tests revealed that the mysterious genetic matter that was released could actually be found throughout her body and was slowly but surely killing her in its expansion. Scully even attempted to adopt the girl, but was initially denied and ultimately unable to when Emily died.

At Emily's funeral, Scully discovered that the body in the casket had been replaced with sandbags - another example of how far the Syndicate was willing to go to ensure the secrecy of their designs. (TXF: "Emily")